Biop-C: A Method for Chromatin Interactome Analysis of Solid Cancer Needle Biopsy Samples
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE166570 | GEO | 2021/09/03
REPOSITORIES: GEO
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Project description:Biop-C: A Method for Chromatin Interactome Analysis of Solid Cancer Needle Biopsy Samples
| PRJNA701288 | ENA
Project description:Transthoracic needle biopsy (TTNB) is integral in the diagnosis and treatment of many thoracic diseases, and is an important alternative to more invasive surgical procedures. Both computed tomography and ultrasound may be used as imaging guidance for TTNB, with CT being more commonly utilized. Needle choice depends mostly upon lesion characteristics and location. During the procedure, patients must be able to follow breathing instructions. Common complications of TTNB include pneumothorax and hemoptysis.
| S-EPMC3140242 | biostudies-other
Project description:Background and Objectives: Endoscopic ultrasound (EUS) fine needle biopsy (FNB) needles were designed to improve histologic yield, while maintaining the flexibility to permit ease of use. However, the diagnostic benefit of EUS-FNB needles as compared to the conventional fine needle aspiration (FNA) needles remains unclear. This study aimed to identify the diagnostic accuracy of combined needle use of a new 20-gauge ProCore FNB needle and a 25-gauge FNA needle. Methods: For this study, cases were selected in which both the 20-gauge ProCore FNB needle and the 25-gauge FNA needle were used during a single EUS procedure for sampling of a solid pancreatic mass, lymph node, or submucosal mass. Tissue acquisition was performed in the course of the ASPRO trial, a multicenter randomized study comparing the diagnostic value of 20-gauge ProCore FNB and 25-gauge FNA needles (ClinicalTrials.gov: NCT02167074). The protocol allowed additional sampling with the nonassigned needle, at the discretion of an endosonographer. Results: Of all 615 patients who were randomized for the ASPRO study, 74 were sampled with both needle types. In these combined needle cases, FNA was used first in 24 and ProCore FNB in 50 cases. Target lesions encompassed 39 solid pancreatic lesions, 18 submucosal masses, and 17 lymph nodes. Most pancreatic lesions were located in the head (25/39), lymph nodes were mainly located in the abdomen (15/18), and submucosal lesions were located in the stomach (8/20), esophagus (4/20), small intestines (3/20), and rectum (3/20). The main reason to use ProCore in addition to FNA was to collect more tissue for ancillary testing (79%). FNA was generally used in addition to ProCore to allow for on-site pathological assessment (76%). The regimen of FNA followed by ProCore resulted in 100% accuracy, while for ProCore followed by FNA, 88% was reached (P = 0.086). The type of target lesion, either pancreatic or nonpancreatic, did not affect the diagnostic accuracy of the two sampling regimens (odds ratio 1.2, 95% confidence interval 0.22–6.61, P = 0.834). Conclusion: FNA followed by ProCore FNB provides for a 100% diagnostic accuracy and tends to outperform ProCore FNB followed by FNA. Accuracy rates were independent of the type of target lesion.
| S-EPMC5569758 | biostudies-literature
Project description:Background and study aims The utility of suction during endoscopic ultrasound (EUS) fine-needle biopsy (FNB) using Franseen-tip needle remains unclear and has not been evaluated in randomized trials. We designed a randomized crossover trial to compare the diagnostic yield during EUS-FNB using a 22G Franseen-tip needle, with and without standard suction. Patients and methods Consecutive patients undergoing EUS-guided sampling of solid pancreatic lesions were recruited. A minimum of two passes were performed for each case: one with 20-mL syringe suction (S+) and another without (S-). The order of passes was randomized and the pathologist blinded. The endpoints were the diagnostic yield and the impact of blood contamination in the diagnosis. Results Fifty consecutive patients were enrolled. The overall diagnostic accuracy was 84 %. A diagnosis of malignancy was obtained in 70 samples: 36 in the S+group and 34 in the S-group. A statistically significant difference was seen in the diagnostic accuracy (S+: 78 % vs. S-: 72 %, P < 0.01) and blood contamination (S+: 68 %; S-: 44 %, P < 0.01). The sensitivity, specificity, negative likelihood ratio and positive likelihood ratio for S+vs. S-samples were 76.6 % vs. 73.9 %, 100 % vs. 100 % and 0.23 vs. 0.26, NA vs NA, respectively. A negative impact of blood contamination in the overall diagnostic yield wasn't seen, even in samples where suction was used (OR 0.36, P = 0.15) Conclusions We found a higher diagnostic yield with the use of suction. It was associated with a higher degree of sample blood contamination that did not affect the diagnostic performance.
| S-EPMC7895663 | biostudies-literature
Project description:BackgroundConventional protocols utilize core needle biopsy (CNB) or fine needle aspiration (FNA) to produce cell suspension for flow cytometry (FCM) is a diagnostic challenge for lymphoid malignancies. We aim to develop an alternative CNB rinsing technique (RT) to produce cell suspension for FCM during this mini-invasive procedure of CNB for lymphoma diagnosis.MethodsFNA and CNB specimens from the same lesion of 93 patients with suspected lymphoma were collected under the guidance of B-ultrasound simultaneously. The fresh CNB samples were prepared to cell suspension by RT for FCM immunophenotyping analysis (Group CNB-RT). Then, the CNB tissues after performing the RT process and the fresh FNA tissues were processed by conventional tissue cell suspension (TCS) technique to obtain the cell suspensions (Groups of CNB-TCS & FNA-TCS), respectively, as comparison. The diagnostic efficacies, as well as the concordances of the FCM results with reference to the morphologic diagnoses were compared in these three groups.ResultsRT could yield sufficient cells for FCM immunophenotyping analysis, though a lower cell numbers compared to TCS technique. The diagnostic concordance was comparable in group CNB-RT (91.1%) to the group CNB-TCS (88.9%) and group FNA-TCS (88.4%) (p = 0.819). The diagnostic sensitivity and specificity of CNB-RT (91.1%; 100%) was not inferior to that of CNB-TCS (88.9%; 100%) and FNA-TCS (88.4%; 98.8%).ConclusionsThis study shows the CNB-RT presented non-inferior diagnostic concordance and efficacy as compared to the TCS technique. CNB-RT has the potential to produce cell suspension for FCM immunophenotyping while preserving tissue for lymphoma diagnosis and research.
| S-EPMC7774716 | biostudies-literature
Project description:The Estrogen Receptor alpha (ERa) is the key transcriptional regulator in luminal breast cancer and the main target for adjuvant treatment. Luminal gene signatures are dictated by the transcriptional capacities of ERa, which are a direct consequence of the receptors binding preference at specific sites on the chromatin. The identification of ERa binding signatures on a genome-wide level has greatly enhanced our understanding of Estrogen Receptor biology in cell lines, but the technique has its limitations with respect its applicability in limit amounts of tumor tissue. Here, we present a refinement of the ChIP-seq procedures to enable transcription factor mapping on limited amounts of tissue culture cells and illustrate the applicability of this refined technology by mapping the ERa genome-wide chromatin binding landscape in core needle biopsy material from primary breast tumors.
2013-04-01 | E-MTAB-1534 | biostudies-arrayexpress
Project description:Endoscopic ultrasound (EUS) with fine needle aspiration (FNA) or biopsy (FNB) to diagnose lesions in the gastrointestinal tract is common. Demand for histology sampling to identify treatment-specific targets is increasing. Various core biopsy FNB needles to obtain tissue for histology are currently available, however, with variable (37-97%) histology yields. In this multicenter study, we evaluated performance, safety, and user experience of a novel device (the puncture biopsy forceps (PBF) needle). Twenty-four procedures with the PBF needle were performed in 24 patients with a suspected pancreatic lesion (n = 10), subepithelial lesion (n = 10), lymph node (n = 3), or pararectal mass (n = 1). In 20/24 (83%) procedures, the PBF needle yielded sufficient material for interpretation (sample adequacy). In 17/24 (71%), a correct diagnosis was made with the material from the PBF needle (diagnostic accuracy). All participating endoscopists experienced a learning curve. (Per)procedural technical issues occurred in four cases (17%), but there were no adverse events. The PBF needle is a safe and potentially useful device to obtain an EUS-guided biopsy specimen. As the design of the PBF needle is different to core biopsy FNB needles, specific training will likely further improve the performance of the PBF needle. Furthermore, the design of the needle needs further improvement to make it more robust in clinical practice.
| S-EPMC8466864 | biostudies-literature
Project description:BackgroundLinear endoscopic ultrasonography (EUS) allows the visualization, identification, and characterization of the extent of lesions of the gastrointestinal (GI) tract and adjacent structures. EUS-guided fine-needle aspiration (EUS-FNA) facilitates a more accurate diagnosis of mediastinal, intra-abdominal, and pancreatic lesions through the collection of the cytological material under direct visualization. Recent reports suggest that histological samples can be obtained by EUS-FNA with a reverse, bevel-tipped needle (the ProCore needle) to collect the core samples (fine needle biopsy, FNB), thereby adding a new dimension to the diagnostic usefulness of this technique. Certain neoplasms, such as lymphoma and stromal tumors, can be assessed by EUS-FNB to confirm the diagnosis. Here, we aimed to carry out a prospective, multicenter, single-blind, randomized, controlled trial to compare EUS-FNB and EUS-FNA.Methods/designA total of 408 patients will be enrolled from five endoscopic centers. Patients will be divided into two groups: (1) group A, which is the EUS regular needle group (EUS-FNA) and (2) group B, which is the EUS ProCore needle group (EUS-FNB). Patients in group A will be examined with a 22G EchoTip Ultra needle, and patients in group B, with a 22G EchoTip ProCore needle. For all included patients, four EUS-guided passes will be made in each lesion. In the first and second pass, a slow-pull suction method of the stylet will be done. The third and fourth pass will use manual suction of 5 cc. The primary objective is to compare the diagnostic yield of malignancy by EUS-FNA versus EUS-FNB.DiscussionThe trial will compare samples obtained by EUS-FNA versus EUS-FNB for the diagnostic yield of solid lesions. The efficacy of these two sampling methods will be assessed on various lesions, which may provide insights into developing practice guidelines for their future indications.Trial registrationClinical Trials.gov, NCT02327065 .
| S-EPMC4830051 | biostudies-literature
Project description:BACKGROUND:The Estrogen Receptor alpha (ER?) is the key transcriptional regulator in luminal breast cancer and is therefore the main target for adjuvant treatment of this subtype. Luminal gene signatures are dictated by the transcriptional capacities of ER?, which are a direct consequence of the receptors binding preference at specific sites on the chromatin. The identification of ER? binding signatures on a genome-wide level has greatly enhanced our understanding of Estrogen Receptor biology in cell lines and tumours, but the technique has its limitations with respect to its applicability in limited amounts of tumour tissue. RESULTS:Here, we present a refinement of the ChIP-seq procedures to enable transcription factor mapping on limited amounts of tissue culture cells as well as from a limited amount of tumor tissue derived from core needle biopsies. Our approach uses a carrier that can be removed prior to DNA amplification and sequencing. CONCLUSION:We illustrate the applicability of this refined technology by mapping the ER? genome-wide chromatin binding landscape in core needle biopsy material from primary breast tumours. With this, our refined technology permits for a high-resolution transcription factor mapping even from clinical samples.
| S-EPMC3637562 | biostudies-literature
Project description:In this work, we report a biopsy-needle compatible rigid probe, capable of performing three-dimensional (3D) two-photon optical biopsy. The probe has a small outer diameter of 1.75?mm and fits inside a gauge-14 biopsy needle to reach internal organs. A carefully designed focus scanning mechanism has been implemented in the rigid probe, which, along with a rapid two-dimensional MEMS scanner, enables 3D imaging. Fast image acquisition up to 10 frames per second is possible, dramatically reducing motion artifacts during in vivo imaging. Equipped with a high-numerical aperture micro-objective, the miniature rigid probe offers a high two-photon resolution (0.833?×?6.11??m, lateral × axial), a lateral field of view of 120??m, and an axial focus tuning range of 200??m. In addition to imaging of mouse internal organs and subcutaneous tumor in vivo, first-of-its-kind depth-resolved two-photon optical biopsy of an internal organ has been successfully demonstrated on mouse kidney in vivo and in situ.
| S-EPMC6325015 | biostudies-literature